GTDB Release 10-RS226 (16th April 2025) has been published
gtdb.ecogenomic.org
gtdb.ecogenomic.org
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 17, 2025 at 12:20 PM
GTDB Release 10-RS226 (16th April 2025) has been published
gtdb.ecogenomic.org
gtdb.ecogenomic.org
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes
Abstract. The Genome Taxonomy Database (GTDB; https://gtdb.ecogenomic.org) provides a phylogenetically consistent and rank normalized genome-based taxonomy
academic.oup.com
October 22, 2025 at 2:20 PM
Our @narjournal.bsky.social manuscript is out! It explores the growth of the GTDB (gtdb.ecogenomic.org) since its inception, as well as updates to the website, methodology, policies, and major taxonomic and nomenclatural changes over the past three years.
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani.
Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....
Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....
GTDB - skani calculator
An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.
gtdb.ecogenomic.org
December 11, 2025 at 2:59 PM
The GTDB website now has an ANI calculator based on skani that supports uploading of user genomes. Try it at gtdb.ecogenomic.org/tools/skani.
Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....
Find more information about @jimshaw.bsky.social fantastic tool at www.nature.com/articles/s41....
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 15, 2026 at 2:06 PM
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 18, 2025 at 7:13 PM
GTDB release 10 based on RefSeq 226 (R10-RS226) is live at gtdb.ecogenomic.org. This release covers 732,475 genomes (22% increase) and has 143,6141 species clusters (37% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r226.
The online ANI calculator (skani) that allows you to compare your genome data with reference sequences in GTDB saves so much time and faffing around. :)
GTDB - skani calculator
An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.
gtdb.ecogenomic.org
February 2, 2026 at 8:27 PM
The online ANI calculator (skani) that allows you to compare your genome data with reference sequences in GTDB saves so much time and faffing around. :)
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
home | GlobDB
globdb.org
June 10, 2025 at 11:20 AM
I'm happy to announce the latest release of the GlobDB, available at globdb.org.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
GTDB release 9 based on RefSeq 220 (R09-RS220) is live at gtdb.ecogenomic.org. This release covers 596,859 genomes (48% increase) and has 113,104 species clusters (33% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r220.
GTDB - R220 Statistics
Statistics describing GTDB release R220.
gtdb.ecogenomic.org
April 24, 2024 at 5:19 AM
GTDB release 9 based on RefSeq 220 (R09-RS220) is live at gtdb.ecogenomic.org. This release covers 596,859 genomes (48% increase) and has 113,104 species clusters (33% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r220.
It’s that wonderful time of year again. A new GTDB release is out :)
GTDB release 11 based on RefSeq 232 (R11-RS232) is live at gtdb.ecogenomic.org. This release covers 901,341 genomes (23% increase) and has 199,923 species clusters (39% increase). Release notes at: forum.gtdb.ecogenomic.org/t/announcing.... Release statistics at: gtdb.ecogenomic.org/stats/r232.
GTDB - Genome Taxonomy Database
The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.
gtdb.ecogenomic.org
April 15, 2026 at 6:07 PM
It’s that wonderful time of year again. A new GTDB release is out :)
Bioinformaticians, you can now use sourmash to search GTDB rs226 reps* with a 10kb+ query in ~15 seconds and 500 MB of RAM, for the low low cost of a 1-time indexing step (2 hrs, 10 GB RAM). See our new HOWTO for using RocksdB indexes!
* You can also search all of GTDB in < 30s.
* You can also search all of GTDB in < 30s.
A quickstart guide to using RocksDB indexing — sourmash 4.9.1.dev0 documentation
sourmash.readthedocs.io
May 20, 2025 at 2:34 PM
Bioinformaticians, you can now use sourmash to search GTDB rs226 reps* with a 10kb+ query in ~15 seconds and 500 MB of RAM, for the low low cost of a 1-time indexing step (2 hrs, 10 GB RAM). See our new HOWTO for using RocksdB indexes!
* You can also search all of GTDB in < 30s.
* You can also search all of GTDB in < 30s.
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io
A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz).
Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz).
Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
Documentation for sylph - ultrafast, precise metagenomic profiling
sylph-docs.github.io
September 15, 2026 at 5:12 PM
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io
A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz).
Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz).
Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes academic.oup.com/nar/advance-... #jcampubs
October 23, 2025 at 5:20 AM
GTDB release 10: a complete and systematic taxonomy for 715 230 bacterial and 17 245 archaeal genomes academic.oup.com/nar/advance-... #jcampubs
GTDB already has one - gtdb.ecogenomic.org/taxon-history
GTDB - Taxon History
Explore how a taxon has changed through GTDB releases.
gtdb.ecogenomic.org
December 13, 2024 at 1:28 PM
GTDB already has one - gtdb.ecogenomic.org/taxon-history
Una rara actuación post-DCD de Peón cantando con la banda de su hermano "Todo por la napia".
www.youtube.com/watch?v=GTDB...
www.youtube.com/watch?v=GTDB...
Miguel Costas 35 Aniversario Todo por la napia con peon kurtz
YouTube video by kLe SCQ
www.youtube.com
September 27, 2026 at 2:15 PM
Una rara actuación post-DCD de Peón cantando con la banda de su hermano "Todo por la napia".
www.youtube.com/watch?v=GTDB...
www.youtube.com/watch?v=GTDB...
10th release & 10th anniversary of developing GTDB (not fully aligned over that time but in sync now). Here’s hoping for another 10 releases/years!
April 18, 2025 at 3:18 AM
10th release & 10th anniversary of developing GTDB (not fully aligned over that time but in sync now). Here’s hoping for another 10 releases/years!
GTDB now indicates the phylogenetic diversity of each phyla: gtdb.ecogenomic.org/stats/r220#p...
September 3, 2024 at 2:47 PM
GTDB now indicates the phylogenetic diversity of each phyla: gtdb.ecogenomic.org/stats/r220#p...
New sylph pre-built databases + taxonomy available for:
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
Sylph-tax - Documentation for sylph - ultrafast, precise metagenomic profiling
sylph-docs.github.io
July 23, 2025 at 2:11 PM
New sylph pre-built databases + taxonomy available for:
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
- GTDB-R226 (143k prok. species)
- GlobDB-R226 (>300k prok. species, thanks @daanspeth.bsky.social )
- UHGV (Unified Human Gut Virome Catalog, thanks @apcamargo.bsky.social )
Must update sylph-tax; see docs (sylph-docs.github.io/sylph-tax/)
8.
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
July 20, 2025 at 1:04 PM
8.
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
GTDB r220 case study (led by @kassipan.bsky.social )
Applied WitChi to the archaeal GTDB r220 supermatrix:
• 5,869 taxa
• 55% of columns pruned
• Biased taxa: 95.1% → 2.3%
• Runtime: <2h on 4 cores
→ Known clades recovered — without using very complex C60 or CAT models
GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/....
Thank you to @ebi.embl.org for support with setting up these links!
Thank you to @ebi.embl.org for support with setting up these links!
ENA Browser
ENA Browser
www.ebi.ac.uk
December 11, 2025 at 3:04 PM
GTDB is now cross-referenced from ENA genome assembly pages. Check it out: www.ebi.ac.uk/ena/browser/....
Thank you to @ebi.embl.org for support with setting up these links!
Thank you to @ebi.embl.org for support with setting up these links!
Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
April 9, 2026 at 9:49 AM
Metabuli & Metabuli App v1.2 improve novel species classification with higher precision and recall. New light mode is 1.8× faster and requires 50% less storage while keeping precision. New RefSeq, GTDB, HRGM, and HROM databases added.
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
💾 github.com/steineggerla...
📄 doi.org/10.64898/2026.03.13.711249
Now available on the Kraken 2 "index zone": a GTDB index! benlangmead.github.io/aws-indexes/k2. It's smaller than the nt index (which we no longer regularly build), but larger than the core_nt index (which we do now regularly build).
Index zone by BenLangmead
benlangmead.github.io
December 13, 2024 at 7:37 PM
Now available on the Kraken 2 "index zone": a GTDB index! benlangmead.github.io/aws-indexes/k2. It's smaller than the nt index (which we no longer regularly build), but larger than the core_nt index (which we do now regularly build).
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
July 20, 2025 at 4:58 PM
Excited to share our work on WitChi! 🛠️🖥️
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
We tested it on the GTDB r220 archaeal supermatrix (5,869 taxa & 10,101 cols) removing 55% of sites in <2h.
The phylogeny showed several interesting groupings with overall improved branch support:
#phylogenetics #ArchaeaSky #MSA #opensource #MEvoSky #MicroSky
Quick blogpost on how to convert the Genome Taxonomy Database (GTDB) protein faa reps into a DIAMOND database that includes taxonomic information and genome ID's
www.jameslingford.com/blog/gtdb-to...
www.jameslingford.com/blog/gtdb-to...
Converting GTDB faa files to a DIAMOND database with taxonomy | James Lingford
Minimal blog by James Lingford
www.jameslingford.com
May 31, 2025 at 12:27 AM
Quick blogpost on how to convert the Genome Taxonomy Database (GTDB) protein faa reps into a DIAMOND database that includes taxonomic information and genome ID's
www.jameslingford.com/blog/gtdb-to...
www.jameslingford.com/blog/gtdb-to...
What is currently the most convenient tool/way to view and explore the bacterial GTDB tree?
November 15, 2024 at 4:15 PM
What is currently the most convenient tool/way to view and explore the bacterial GTDB tree?
Looks like in GTDB release 226 the Bacillota_A to H crowded field has merged once more into a single phylum! What's the reasoning @xrefugee13.bsky.social?
July 22, 2025 at 2:36 PM
Looks like in GTDB release 226 the Bacillota_A to H crowded field has merged once more into a single phylum! What's the reasoning @xrefugee13.bsky.social?